->> Doug, can not get to talk to repair people. Just the call center folks who only have a piece of paper in front of them.
Shutter was blown up, so that may have caused the issue.
A bit frustrating that I can not talk to someone on the repair bench to get a clearer understanding of how it happened. Repair estimate is $1,275 for a camera worth $1,200.00. Decisions, decisions.

->> Someone correct me. My understanding is that most would have a filter covering the actual sensor....

$1275 for a $1200 body - for me that wouldn't be much of a decision. Especially if it were a Canon MKIV and I was still using the original battery technology. Just upgrading the battery to the smart one and getting a new charger would set you back nearly $700. I almost upgraded just because of that.

->> Not terribly uncommon with shutter failures. Had it happen to a body recently, the shutter violently failed, and one of the blades scraped across the sensor as a result. New shutter and new sensor needed.

Which brand/model camera is it? If it a Canon or most Nikons, then Alan's assertion about a filter over the sensor would be correct. But if you're using a Nikon D810 then there is no filter which would result in direct sensor damage. OR, is the filter part of the sensor unit where if the filter is damaged you have to replace the sensor too.

You are correct, there is a filter over the sensor. That being said, with Canon it is hermetically sealed to the sensor, so, if you replace the filter, you replace the sensor. This happened on a 5D2 that was sent into CPS. A $600 repair for just the sensor + I forget the additional amount for the shutter.

Scratches can also come from dragging large pieces of dust (like sand) across the filter.

I would only replace it if you can see the scratch in your images. Otherwise I don't see any added value in replacing it if only a tech can see it.

I'm not a Nikon person, so you may want to check that about the D810. 10 seconds googling the answer finds in fact there is some sort of glass over the sensor. It would be REALLY hard to clean photo sites if there were no glass and the sensor were left open to dust. There is always some kind of filter, or cancellation filter.

Yes, there is protective "glass" over the D810 sensor but not a "filter" which is normally thought of as an anti-aliasing filter to diminish moire. As to whether the glass is replaceable, I have no clue -- nor do I want to think about it.

->> I aim to please. But really, I'm seeing deals on eBay for $900 and below on a used D3 and about 1,200 for a D3s (though they are harder to find at that price, I've seen auctions end that low). I think a current SS.com member has a D4 for 1,500 right now. So really you're in the ballpark for an upgrade.

->> Going to talk to NPS Monday morning and see if I send it in again if I can get a more definitive answer this time. If not, a ton of D3 bodies are out there for $300-$400 less than the estimate, Nice looking paper weight though!